--- Log opened Fri Feb 08 00:00:54 2013
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00:46 < nmz787> why wasn't the bio tech n beyond thing advertised on the diybio list?
00:48 < kanzure> because people like keeping secrets, for whatever reason
00:48 < nmz787> :(
00:48 < kanzure> nmz787: you should post this,
00:49 < kanzure> http://www.utsandiego.com/news/2013/jan/26/do-it-yourself-biotech-spread
00:57 < kanzure> nmz787: the biggest single thing that perpetuates all types of abuse is silence, post it.
00:57 < kanzure> i don't know why joe put up with all the bullcrap at biocurious; he had wonderful ideas from the beginning and he let them go down the drain.
00:59 < kanzure> "Regional DIYbio lists splinter the community" damn straight
01:14 < nmz787> kanzure: have any jobs for me?
01:15 < nmz787> por dinero
01:15 < superkuh> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=865219
01:15 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/a28c1eb3c7b19a872e63638fe51da48a.txt
01:16 < superkuh> paperbot: http://ieeexplore.ieee.org/ielx5/8/18731/00865219.pdf?tp=&arnumber=865219&isnumber=18731
01:16 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/645fccb72fee4c4e026e0edff028ed9c.pdf
01:22 < superkuh> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=959755
01:22 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/ef740d96e21a66fc1cc8b219575729fb.txt
01:22 < superkuh> paperbot: http://ieeexplore.ieee.org/ielx5/7598/20720/00959755.pdf?tp=&arnumber=959755&isnumber=20720
01:22 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/9353712cb2e6e26e9b83725f7c4c20d8.pdf
01:22 < superkuh> Sorry about the spam.
01:23 < kanzure> that's what it's here for
01:34 < nmz787> superkuh: quit spamming us with knowledge
01:36 < kanzure> nmz787: i'll do the math on whether or not it would make sense for me to pay you to do things, give me a few days of number crunching.
01:37 < nmz787> kanzure: cool, i actually just stumbled on a linkedin job posting that actually excites me a bit
01:38 < nmz787> if they don't get back to me, I think I might drop by on them in person
01:38 < kanzure> ha ha ha
01:38 < kanzure> http://www.soothetube.com/2013/01/29/interview-with-henry-markram/
01:39 < kanzure> " He also appears to have a bit of a Captain James T. Kirk thing going on with his hairdo….circa Star Trek: The Wrath of Khan (see below)"
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01:47 < nmz787> kanzure: so if you're on every list, you should be the cross-posting bot
01:48 < nmz787> kanzure: or have a list of the lists you're subscribed to
01:48 < kanzure> nmz787: http://heybryan.org/mailing_lists.html
01:48 < kanzure> but it's about 3 years old at this point
01:48 < nmz787> d'oh
01:49 < kanzure> On Fri, Feb 8, 2013 at 3:41 AM, Cathal Garvey <cathalgarvey@cathalgarvey.me> wrote:
01:49 < kanzure> > That'll be why you're subscribed to virtually every mailing list I've
01:49 < kanzure> > ever encountered, then? :)
01:49 < kanzure> Bryan Bishop is actually a fictional character owned wholly by Marvel Entertainment, Inc.
01:49 < nmz787> lol
01:50 < kanzure> i sold my soul for a $0.50 comic, you see..
01:52 < nmz787> first edition?
01:55 < kanzure> diybio--seattle, diybio-sf, diybio-boston, diybio-london, diybio-nyc, diybio-hifive, diybio-eu, diybio-ireland, diybio-vancouver, diybio-austin, biocurious, biologigaragen, biohacksyd, biohacklab, there's a bunch of other group-lists i'm forgetting
01:55 < kanzure> http://diyhpl.us/wiki/diybio/groups has a better list i think
01:56 < kanzure> oh also the la group, hrm
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02:00 < kanzure> 14 mailing lists are listed on that page (just on groups.google.com; there might be some hosted on other servers)
02:02 < kanzure> ah also east-bay-diybio
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02:10 < superkuh> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5171599
02:10 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/dbee895ccc30db8fcd5630eebf7184f3.txt
02:10 < superkuh> paperbot: http://ieeexplore.ieee.org/ielx5/5154401/5171433/05171599.pdf?tp=&arnumber=5171599&isnumber=5171433
02:11 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/3a9428ced5353164aa42c385e823f66a.pdf
02:18 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=c48a377f Bryan Bishop: better support for IEEE Xplore
02:18 < gnusha> paperbot: reload papers
02:18 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-02-08 10:18:20)
02:18 < kanzure> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5171599
02:18 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/e4f1417cb39f772faeb35a3d56f559f3.txt
02:21 < kanzure> well that failed. i wonder what went wrong.
02:22 < kanzure> the architecture is broken anyway..
02:22 < superkuh> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=610834
02:22 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/26cf2eb5ba41c463a16cc7c00823bac1.txt
02:22 < superkuh> paperbot: http://ieeexplore.ieee.org/ielx3/4819/13320/00610834.pdf?tp=&arnumber=610834&isnumber=13320
02:22 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/411bfb5815fdd38dce64d67a3d4dd59b.pdf
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02:47 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=d400040c Bryan Bishop: an even better IEEE fix
02:47 < gnusha> paperbot: reload papers
02:47 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-02-08 10:47:53)
02:48 < kanzure> paperbot: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=610834
02:48 < paperbot> http://diyhpl.us/~bryan/papers2/paperbot/b2dcce881ad3694a94e73b44083f8ae5.pdf
02:48 < kanzure> much better.
02:48 < kanzure> someone should rewrite all of that before it becomes unsalvagable crap.
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02:50 < nmz787> kanzure: is it lame to want to call my project openSpectrometer
02:50 < nmz787> rather than Open Spectrometer
02:51 < kanzure> yes, but i wasn't going to bring it up because in the scheme of things i'd rather have a working open source spectrometer
02:52 < nmz787> why don't you like it?
02:52 < nmz787> as far as a title, a logo?
02:52 < kanzure> because it doesn't match any other naming conventions
02:52 < nmz787> what naming conventions?
02:53 < nmz787> other spectrometers are called USB 2000
02:53 < nmz787> USB2000
02:53 < kanzure> other spectrometers are proprietary junk named by monkeys, you shouldn't use those as role models anyway
02:53 < kanzure> Biooo Hazard Elite spectrometer 199x
02:53 < archels> SpectrOpenMeter
02:54 < archels> well, maybe not
02:55 < nmz787> ugghh
02:55 < kanzure> another issue is that i'm not sure what open source license you applied to your work so far
02:55 < nmz787> openSpectrometer seems less formal than Open Spectrometer
02:55 < kanzure> iirc it wasn't something OSI approved but i might be mistaken
02:55 < nmz787> but not crazy weird either
02:55 < nmz787> OSI?
02:55 < archels> any product whose name includes "2000" has to be made of win, though.
02:55 < kanzure> OSI was a random group that formed to popularize the term "open source"
02:56 < nmz787> ahh
02:56 < archels> kanzure: are they still bickering about the Open Source Hardware logo (the open cog)?
02:56 < kanzure> fun fact: chris petersen from foresight nanotech institute was part of OSI
02:56 < kanzure> archels: no clue
02:56 < kanzure> they just got together to define what they wanted open source to mean
02:56 < kanzure> so it's nice to have something to point to
02:57 < kanzure> juri_ is going to eat my balls for breakfast when she reads this, though (since she prefers the licensing from FSF)
02:57 < kanzure> i can only pray that her lethargy will keep her from reading the backlogs
02:58 < archels> not mentioning her name might also help in the future
02:58 < kanzure> i am not a very good strategist at 5am
02:59 < nmz787> psh, it's 2:50 here
02:59 < nmz787> 2:59*
02:59 < kanzure> time travel?
02:59 < nmz787> yes
02:59 < nmz787> i can call the future too
03:00 < nmz787> my indian connection
03:00 < kanzure> archels: i know what nmz787 is doing up, but what about you?
03:03 < archels> I live in The Netherlands, it's 12 o'clock here
03:03 < archels> noon, that is
03:03 < kanzure> do you know pieter van boheemenienen
03:04 < archels> never heard of the guy. *googles*
03:04 < kanzure> ieter van Boheemen <pieter.van.boheemen@amplino.org>
03:04 < kanzure> ack
03:04 < kanzure> Pieter
04:03 < kanzure> eleitl: alive?
04:03 < nmz787> gosh its late
04:03 < nmz787> kanzure: i am reformatting this, check out the diff http://openspectrometer.com/test.php
04:03 < ThomasEgi> juri_, i'm done etching and soldering my circuit. now... i could make good use of a printed case ;)
04:04 < kanzure> nmz787: i am strongly opposed to php
04:05 < kanzure> i also suggest not restricting the content to the middle of the page
04:06 < nmz787> php is just for some email function
04:06 < kanzure> you can host webpages on github on a gh-pages branch btw
04:06 < nmz787> why?
04:06 < nmz787> i mean why would i do that?
04:06 < kanzure> because it's a simple way to do version control of a website
04:06 < kanzure> also, all repositories on diyhpl.us have an ikiwiki instance
04:07 < kanzure> it's just a suggestion, not mission critical at the moment
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04:17 < kanzure> i think eleitl is in email mode
04:19 < kanzure> hmm http://neuronvisio.org/screenshots.html#network-example
04:19 < kanzure> these do not look histologically realistic
04:19 < archels> hah
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07:09 < juri_> kanzure: i read all of the backlogs. ;)
07:15 < juri_> I'd much rather one of the OSI aproved licenses than NOT one of the OSI approved licenses. yes, i avoid contributing to non-gpl work.. but free-er is free-er. as you were saying earlier, the other options are proprietary piles of wizbang marketing 101. an Open option is better than none.
07:15 < juri_> just expect people like myself to be staring at it, wanting a Free option. ;)
07:15 < juri_> thomas: got a case design? i'm due to fire my plastic printer up soon.
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07:59 < ephialtes480> paperbot: http://www.medscape.com/viewarticle/772502_3
07:59 < paperbot> TypeError: argument of type 'NoneType' is not iterable (file "/srv/ikiwiki/paperbot/modules/papers.py", line 171, in download_url)
07:59 < ephialtes480> paperbot: https://www.thieme-connect.de/ejournals/pdf/10.1055/s-0032-1324717.pdf
07:59 < paperbot> TypeError: argument of type 'NoneType' is not iterable (file "/srv/ikiwiki/paperbot/modules/papers.py", line 171, in download_url)
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09:16  * eleitl is alive
09:19 < ThomasEgi> eleitl, good job!
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09:42 < AlonzoTG> eeek.
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10:58 < archels> wow, the OpenWorm people are planning on using PSICS as their neuronal simulator?
10:58 < archels> They do realise that every single ion channel is a discrete entity there, hopefully?
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11:33 < archels> "I've never been a fan of neural nets." --Ray Kurzweil (2012)
11:33  * archels hatin'
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11:38 < juri_> i'm not a fan of his neural net. is that close?
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12:40 < archels> www.turingbirds.com/temp/cannon.png
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13:26 < gnusha> https://secure.diyhpl.us/cgit/paperbot/commit/?id=bef66e12 Bryan Bishop: citation_pdf_url is not always available
13:26 < gnusha> paperbot: reload papers
13:26 < paperbot> gnusha: <module 'papers' from '/srv/ikiwiki/paperbot/modules/papers.py'> (version: 2013-02-08 21:26:44)
13:27 < kanzure> paperbot: http://www.medscape.com/viewarticle/772502_3
13:27 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/ac4a3a65066eb796250c17ce652809e6.txt
13:27 < kanzure> paperbot: https://www.thieme-connect.de/ejournals/pdf/10.1055/s-0032-1324717.pdf
13:27 < paperbot> no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/6d9863111a6b756e8e6d9329a176009d.txt
13:28 < kanzure> "Thieme E-Journals - Seminars in Reproductive Medicine / There is no PDF availalbe for this article."
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13:52 < nmz787> SECRETS KEEP US SICK... is a slogan thrown around at mental rehabs
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13:54 < kanzure> nmz787: is it?
13:54 < kanzure> why?
13:58 < nmz787> I think it's generally like your comment 00:57 < kanzure> nmz787: the biggest single thing that perpetuates all types of abuse is silence, post it.
13:58 < nmz787> secret==silence
13:58 < nmz787> or at least secret==lack-of-transparency
14:01 < kanzure> oops, i meant, post the article :P
14:01 < kanzure> which you did
14:02 < kanzure> also, what makes a sound in a car that sounds like a flat tire but isn't?
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14:24 < jrayhawk> CV joint failure, maybe?
14:25 < jrayhawk> I assume it's at wheel speed.
14:25 < jrayhawk> or, rather, modulated by wheel speed.
14:25 < kanzure> yes
14:25 < kanzure> maybe it's a flat, and i just can't tell yet.
14:25 < jrayhawk> air pressure guages are cheap and handy
14:25 < kanzure> yeah i have one somewhere.
14:27 < jrayhawk> If you're getting bad vibration through the steering wheel at highway speed, then a wheel weight might've fallen off or a rim might've gotten bent.
14:27 < nmz787> CV joint would be clicking, the broken/failing side is indicated by driving in a circle (steering wheel turned fully), the failing part os the side you're turning away from (the side that is loaded with weight during the turn)
14:28 < nmz787> failing part is on the side you're turning away from
14:28 < nmz787> kanzure: what do you mean it sounds like a flat, like a rubbing sound?
14:28 < nmz787> i guess i've never really had a flat
14:28 < nmz787> at least in a while
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14:29 < nmz787> maybe the emergency brakes are dragging
14:29 < nmz787> maybe you're driving with the e-brake engaged?
14:29 < eudoxia> archels: i wonder what he is a fan of
14:29 < nmz787> is the brake light illuminated on the control panel?
14:29 < eudoxia> other than his "let them eat FLOPS" roadmap for posthuman intelligence
14:30 < nmz787> FLOPjacks
14:31 < jrayhawk> And diffs and final drive gears can go bad in similarly funny ways, but that's somewhat less likely than CV joint.
14:37 < kanzure> jrayhawk: nah, no vibrations
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14:42 < nmz787> someone i know advocates for adding piezoelectric microphones to various parts of the car to fingerprint various vehicle health states
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14:46 < kanzure> nmz787: piezos make the world better.
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14:58 < nmz787> jrayhawk: is the right side of the car the driver or passenger?
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15:00 < nmz787> seems in the U.S. the right side is the passenger side
15:00 < nmz787> from the perspective of sitting-in-the-driver
15:00 < nmz787> driver's seat
15:01 < Urchin[Emacs]> it's based on the side of the road one drives on
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15:01 < Urchin[Emacs]> if the cars drive on the left, the driver side is on the right, and vice-versa
15:02 < nmz787> Urchin[Emacs]: the problem I was having was that some parts were listed as right-side vs left-side
15:03 < nmz787> but i wasn't sure if it was looking at the car from the front (while working in the engine bay), or while sitting in the car
15:04 < Urchin[Emacs]> it's usually from the perspective of the person sitting, afaik
15:04  * Urchin[Emacs] is not in america
15:05 < nmz787> Urchin[Emacs]: yeah that's what google tells me
15:07 < Urchin[Emacs]> google?
15:07 < nmz787> 'is the right side of the car the passenger side'
15:07 < nmz787> 'When ordering side specific items, typically, side is meant "as you sit in the drivers seat"'
15:07 < nmz787> first hit
15:07 < Urchin[Emacs]> right
15:08 < Urchin[Emacs]> do you know why the sides where people drive are as they are?
15:08 < nmz787> i've heard it before
15:08 < nmz787> cant remember now
15:09 < Urchin[Emacs]> while coaches were still used people drove on the left because a right-handed person could use the sword that way
15:09 < nmz787> lol
15:09 < Urchin[Emacs]> but Napoleon changed the rules and made people drive on the right
15:10 < Urchin[Emacs]> Hitler also perpetuated the reform
15:10 < kanzure> "Prior to its scheduling, it was part of a number of supplements that were seized during FDA enforcement of Bodybuilding.com for selling unapproved new drugs."
15:10 < kanzure> bodybuilding.com was busted by the FDA?
15:11 < Urchin[Emacs]> bodybuilding suplements have proven to be fatal at times, afaik
15:22 < kanzure> so?
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15:31 < nmz787> hot damn
15:31 < nmz787> ""
15:31 < nmz787> 8.  Understand that synthetic biology is trying to understand the mind of God.  This is also heresy in the biological community as most are darwinists and refuse to acknowledge a creator.  When you realize this it helps you really think outside the box.  For example, understand that nature is using quantum mechanics to select for fitness.  God wrote DNA and setup all the systems that cause life to work.  It is not wasteful or inneficient.  I absolute
15:35 < Urchin[Emacs]> I once found someone saying that evolution could only be compared to Azathoth
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15:40 < kanzure> nmz787: what are you quoting?
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16:00 < nmz787> kanzure: william heath
16:00 < nmz787> see the latest DIYbio post
16:00 < nmz787> well, second to last now
16:01 < nmz787> kanzure: i guess I just exposed on DIYbio that I'm not a firm believer in God
16:01 < kanzure> wow xp_prg said that? that's hilarious.
16:02 < kanzure> you weren't around, but he used to curse this channel with his presence.
16:02 < nmz787> who?
16:02 < kanzure> anyway, i'm sure the majority of diybio participants are either agnostic, atheist, or careful enough to not write such spurious crap
16:02 < kanzure> xp_prg is william heath
16:02 < nmz787> kanzure: ahh
16:03 < kanzure> i don't see your response to him
16:04 < kanzure> xp_prg has always been very angry that nobody can give him a single-button solution to biology
16:05 < nmz787> kanzure: i have his phone num
16:05 < nmz787> :P
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16:05 < kanzure> "The biology field and most of the people in the field are not computer scientists and are very shocked to discover that cells are actually hardware (cells) executing programs (dna). "
16:05 < kanzure> haha.. that's not entirely true though.
16:05 < nmz787> kanzure: https://groups.google.com/d/msg/diybio/ajOF_600gVQ/OC-bfZnoMqgJ
16:05 < kanzure> i mean, that's not how programming works, and it's not how biology works.
16:06 < kanzure> "They are not skilled in the arts of computer science and quickly overwhelmed by these advanced concepts/approaches." pfft.. it's not advanced at all.
16:06 < kanzure> "Keep this in mind when working with them as you are massively disrupting the entire field." what disruption is he talking about.. the concept of software?
16:06 < nmz787> kanzure: well to be fair you had some trouble a week or two ago understanding why I wouldn't wipe windows from my dad's machine and put linux on it
16:07 < nmz787> kanzure: so programming is definitely a valid out-of-paradigm area for a lot of biologists
16:07 < ephialtes480> kanzure: does pdfparanoia, when it remove_object_by_id also update the xref array to reflect the new byte offsets of the remaining objects?
16:07 < nmz787> i think synBio
16:08 < kanzure> you didn't want to wipe the os because you were angry with me, not because it was a bad idea
16:08 < kanzure> ephialtes480: no. i don't think they are byte offsets anyway. i thought they were ids.
16:08 < nmz787> kanzure: wrong, because my dad wouldn't be happy with linux
16:09 < nmz787> kanzure: eleitl even popped in to add regarding that
16:09 < kanzure> ah sorry, the dad situation. i meant the spectrometer situation.
16:09 < kanzure> i am somewhat concerned that the email you linked to hasn't arrived in my inbox
16:09 < nmz787> err
16:09 < nmz787> hmm
16:10 < nmz787> kanzure: was that the crisis you mentioned, email space?
16:11 < kanzure> i don't know, i am receiving other emails so i'm tryign to figure out what's going on
16:11 < kanzure> for whatever it's worth, i think your reply is okay
16:11 < ephialtes480> kanzure: the xref array gives you an id of the object, and then where to find it (they are not in order usually). So looking at the (pre-strapped) PDF, if you:  dd if=my.pdf bs=1 skip=[THE BYTE OFFSET OF THE OBJECT IN XREF ARRAY] 2>/dev/null | less - you will see where the object is. I'm getting some problems with corrupted PDFs and wondering if the post-strip inaccuracy of the "table of contents" that is the xref array at the end might be the
16:12 < kanzure> nmz787: i also like to link to this one,
16:12 < kanzure> https://groups.google.com/forum/#!msg/diybio/GxRTESzUWUI/X9dro2viFCcJ
16:12 < kanzure> ephialtes480: huh, interesting. so far i have just been stripping out objects and everything works fine.
16:13 < kanzure> aha now i have your email
16:13 < ephialtes480> ya, that seems to suggest my theory is wrong. I'm just trying to work out why I'm corrupting everything with a custom single-file version of your script I'm using to reconnoiter PDFs from other databases. Perhaps if I send you the script you can spot where the corruption is arising from? It is 90% your code
16:14 < nmz787> kanzure: yesh that's a good post too
16:14 < ephialtes480> my email?
16:14 < kanzure> ephialtes480: nah, nmz787 sent one out https://groups.google.com/forum/#!msg/diybio/ajOF_600gVQ/OC-bfZnoMqgJ
16:15 < ephialtes480> ah! :)
16:15 < kanzure> nmz787: also, this line is pretty funny :) "Seems like you're ignoring the folks who had the same idea in that  PNAS paper linked via the DIYbio discussion comparing E.coli to linux, as well as Anselm who directly engaged you in that discussion. Seems like you're saying you have secret knowledge that other's in the field don't have, this sounds like the tenure-track professors you complained about."
16:17 < ephialtes480> Well, I'm calling it a night. I put the test script (my first ever script in python, mostly your code though) here: https://anonfiles.com/file/08973f512071958c413725d906ba8044 (it outputs the PDF with target objects stripped but corrupted. Format of the command is: pdftest.py [search|remove] [filename] [search term]
16:18 < nmz787> ephialtes480: congrats on learnding python
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16:20 < ephialtes480> it is mess, my code (in any programming language) is full of inefficiencies, repetitiveness and unecessary nonsense...I'm just happy when they finally work most of the time.
16:20 < ephialtes480> but thx nmz
16:20 < ephialtes480> and to you kanzure for always taking time to answer qs.
16:21 < kanzure> yashgaroth: hello
16:21 < yashgaroth> yo
16:21 < kanzure> yashgaroth: today's humor is provided to you by xp_prg, xist because of
16:21 < kanzure> the work traditional biologists and chemists have done, don't scoff at
16:21 < kanzure> them because their method for uncovering knowledge seems awkward in
16:21 < kanzure> hindsight. The paradigms have served well in the past, that doesn't
16:21 < kanzure> oops
16:22 < kanzure> terrible paste
16:22 < kanzure> https://groups.google.com/d/msg/diybio/ajOF_600gVQ/T5rSMt05BGMJ
16:22 < yashgaroth> oh dear I'll give it a read
16:23 < yashgaroth> also I need to see if I can dig up what plasmid this phillyj person is working on/having problems with
16:23 < yashgaroth> since 'low endotoxin, high supercoiled' plasmid is only used for one thing
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16:26 < kanzure> haha "Brownian motion is the world wide web of the cell"
16:27 < nmz787> yashgaroth: which one thing?
16:27 < yashgaroth> in vivo use
16:28 < yashgaroth> specifically, gene therapy or dna vaccine
16:28 < nmz787> is sex an in-vivo use of a penis?
16:28 < yashgaroth> I'll do a study
16:29 < yashgaroth> I suppose they could be trying to transfect sensitive immune cells in vitro, but even then no one gives a fuck about the supercoiled percentage
16:32 < abetusk> Does anyone have any information on either cheap pH probes or a DIY method of producing your own?
16:33 < yashgaroth> I do wonder if someone's made a smartphone app to read pH strips
16:35 < nmz787> abetusk: indicator dye? bromocresol green is pretty cheap
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16:36 < abetusk> I'm sorry, I should have said re-usable
16:37 < yashgaroth> there's some pretty cheap ones on amazon
16:37 < abetusk> re-usable and electronic
16:38 < yashgaroth> they're all electronic
16:38 < abetusk> re-usable then
16:38 < yashgaroth> well the meters on amazon are also all reusable
16:39 < kanzure> http://gowers.wordpress.com/2013/01/28/the-elsevier-boycott-one-year-on/
16:39 < nmz787> abetusk: hanna ph checker is one that's been around for a while
16:39 < nmz787> abetusk: this too https://www.sparkfun.com/products/10972
16:39 < abetusk> At some point the bio chips will have to measure pH.  What method are they going to use for that?  Just strips?
16:40 < nmz787> abetusk: http://www.sparkyswidgets.com/Products/Store/Details/tabid/81/ProductID/4/Default.aspx
16:40 < yashgaroth> what bio chips
16:41 < nmz787> abetusk: if i wanted to measure pH on a lab-on-a-chip I'd have to fabricate the pH sensor on the chip
16:41 < nmz787> abetusk: http://en.wikipedia.org/wiki/Silver_chloride_electrode
16:41 < kanzure> yikes that anti-elsevier statement is signed by john baez
16:42 < nmz787> abetusk: http://en.wikipedia.org/wiki/PH_meter
16:42 < nmz787> abetusk: http://en.wikipedia.org/wiki/Glass_electrode
16:43 < abetusk> nmz787, thanks, I've seen the wikipedia articles.  I was looking for something that could be done in miniature, re-usable and preferably be gotten for cheap or made myself
16:44 < abetusk> There's a sensor based on isfet technology, but I don't really know that much about it
16:46 < klafka_> hey kanzure what were the other multiprocessing libs you recommended other than multiprocessing?
16:46 < kanzure> klafka_: gevent, eventlet
16:46 < klafka_> do they manage process memory management better?
16:47 < kanzure> not sure
16:47 < kanzure> there was a good study in 2009 that someone did, but that was 2009.
16:47 < kanzure> these days i see a lot of people recommending gevent
16:47 < klafka_> ah i see
16:47 < kanzure> the problem with other libraries (not gevent or eventlet) is that they use an entire python instance per thread or coroutine
16:48 < kanzure> gevent does not; it just switches opportunistically between coroutines under a single python instance.
16:48 < kanzure> something based on libevent
16:48 < kanzure> or libev. not sure which one.
16:48 < klafka_> ummm
16:49 < klafka_> kanzure:  this doesn't seem effective for like multi-core mapreduce sort of shit
16:50 < kanzure> perhaps not, there's probably better ideas out there
16:54 < nmz787> abetusk: miniature is a big world
16:54 < nmz787> abetusk: i'm sure the isfet's that ion torrent uses are cheap, and they're probably reusable (though the chip might not support that)
16:55 < nmz787> abetusk: you could manufacture a AgCl electrode on a lab-on-a-chip
16:56 < nmz787> abetusk: i.e. http://www.bioee.ee.columbia.edu/courses/upload/Bibliography/Polk_AgAgCl_microelectrodes_sensact.pdf
16:57 < nmz787> abetusk: didn't you add depth detection to a PCB mill?
16:57 < nmz787> using resistance?
16:58 < abetusk> it's a continuity test, but yes, depth detection for a PCB mill
16:58 < abetusk> I just made my first functioning circuit the other day
16:58 < abetusk> through hole, but still
16:59 < nmz787> abetusk: http://144.206.159.178/FT/120/599693/12462462.pdf
16:59 < nmz787> abetusk: Microuidic pH-sensing chips integrated with pneumatic
16:59 < nmz787> uid-control devices
17:00 < nmz787> kanzure: that's the same site I found the other day!
17:01 < kanzure> nmz787: http://scholar.google.com/scholar?q=site%3Ahttp%3A%2F%2F144.206.159.178%2FFT&
17:02 < nmz787> paperbot: http://pubs.acs.org/doi/abs/10.1021/ac9007573
17:03 < paperbot> error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Electrochemical%20Detection%20for%20Paper-Based%20Microfluidics.pdf
17:03 < abetusk> nmz787, thanks, that's what I was looking for
17:03 < nmz787> kanzure: thanks, google works better than their on-site search
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17:15 < nmz787> i don't like that government entities ask me to press 1 for english
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17:48 < kanzure> "The one million dollar ($1,000,000) prize will recognize ... Novel technologies to enhance human brain function, .... Novel brain stimulation technologies, ... Novel brain-machine interface technologies." http://www.israelbrain.org/global-braintech-prize/competition-overview/
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18:13 < kanzure> "Jboss, running on JDK, is vulnerable to SQL injection. A remote attacker could send a sequence of SQL commands to TCP port 1701 to obtain"
18:13 < kanzure> well alright then
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18:25 < nmz787> kanzure: can you fork/copy this https://bitbucket.org/chapmanb/synbio/src/7b1b3a972b7e/SynBio?at=default
18:33 < kanzure> sure, things on bitbucket are either hg or git
18:33 < kanzure> "ADAMS adheres to security standards similar to those found in the banking industry. ADAMS uses 128-bit SSL encryption to protect data transmissions."
18:33 < kanzure> the anti-doping industry is a joke.
18:34 < yashgaroth> I wonder if anyone would be willing to set up an alternative league without testing
18:35 < kanzure> it's a little weird to me how they all got together to form an international anti-doping enforcement agency..
18:35 < yashgaroth> saves labor
18:38 < kanzure> it also looks like this site is possibly hackable
18:38 < kanzure> i think they have basically all athletes listed here with addresses and time-of-day availability for testing
18:39 < kanzure> "You are required to include on your ADAMS whereabouts a 1 hour testing slot – for each day. (7 days a week) of the next quarter (e.g. January-March 2013),"
18:40 < yashgaroth> what's the high security for? access to top athletes' location?
18:40 < kanzure> and which drugs they are positive for
18:40 < kanzure> i wonder how corrupt this system is
18:41 < nmz787> hmm, actually kanzure I can't tell but that code might not be so great
18:42 < kanzure> http://www.youtube.com/watch?v=UmTpHy9oJc8#t=400
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18:50 < kanzure> geeze look at page 71
18:50 < kanzure> http://www.wada-ama.org/Documents/ADAMS/Training_User_Guides/ADAMS%20User%20Guide%20-%20Accredited%20Laboratories%20POST%20V3.2%20HOTFIX2%2016-11-2012.pdf
18:50 < kanzure> 'athlete biological passport'
18:55 < nmz787> this is phenomenal http://www.thedailyshow.com/watch/thu-february-7-2013/tanks--but-no-tanks
18:55 < nmz787> .title
18:55 < yoleaux> Tanks, But No Tanks - The Daily Show with Jon Stewart - 02/07/13 - Video Clip | Comedy Central
18:56 < kanzure> geeze they also track chess athletes
18:56 < kanzure> and cricket?
18:56 < yashgaroth> cricket's pretty big
18:56 < kanzure> and "electronic sports" or.... "esports"
18:57 < kanzure> "firefighting and rescuing".. oh come on, what the fuck guys.
18:57 < kanzure> "wheelchair fencing".. ok fair.
18:57 < kanzure> http://web.archive.org/web/20120723013937/http://www.wada-ama.org/Documents/ADAMS/Training_User_Guides/ADAMS%20Import%20Codes%20for%20Sport,%20Discipline,%20Country,%20Region%20V2.5.pdf
18:58 < kanzure> "life saving, pool". what...
18:59 < kanzure> i have no idea why firefighting would be managed by the world anti-doping association
18:59 < kanzure> but at least keyboard typing is not listed. i'm safe.
19:01 < nmz787> "if you're a muslim, you'd better be out there jihaading away"
19:01 < nmz787> i think that's what he says around 3:05
19:01 < yashgaroth> 420 jihad every day
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19:08 < kanzure> page 30 has a password:
19:08 < kanzure> http://web.archive.org/web/20100216235346/http://www.wada-ama.org/Documents/ADAMS/Training_User_Guides/ADAMS_User_Guide_Sporting_Organizations_V2_2_NL.pdf
19:08 < kanzure> and so does the following page
19:09 < kanzure> they seem to be <first initial><last initial><2-digit month><2-digit day><4-digit year>
19:10 < juri_> http://www.wired.com/design/2012/11/3-d-printed-cartilage/
19:11 < juri_> i know, kindof old news, but news to me.
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19:41 < kanzure> http://www.presagia.com/1599 the wada/presagia announcement
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20:35 < nmz787> kanzure: earlier you mentioned netflix i think?
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20:43 < kanzure> nmz787: what about it
20:43 < kanzure> BioGuy: hi
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20:54 < BioGuy> Hey!
20:54 < BioGuy> nmz787 - did you just post the other day on google groups?
20:58 < jrayhawk> He did! I saw it!
20:58 < jrayhawk> I'll testify to it in court!
20:59 < jrayhawk> GET THE PITCHFORKS
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21:00 < nmz787> BioGuy: hi
21:00 < nmz787> kanzure: do you watch it on linux?
21:00 < nmz787> BioGuy: I post all the time on google groups
21:00 < nmz787> like its my job
21:01 < nmz787> BioGuy: I think I even emailed you personally a few months ago, and never heard back... what's happening?
21:02 < nmz787> BioGuy: I've tried emailing and IRCing with the hackerspace people here, but there isn't much activity
21:03 < kanzure> nmz787: android-x86
21:04 < kanzure> actually that's wrong, it doesn't work on android-x86 because their binaries are compiled for arm i think
21:09 <@fenn> i got a kick out of this: "Understand that synthetic biology is trying to understand the mind of God.  This is also heresy in the biological community as most are darwinists and refuse to acknowledge a creator.  When you realize this it helps you really think outside the box.  For example, understand that nature is using quantum mechanics to select for fitness.  God wrote DNA and setup all
21:09 <@fenn> the systems that cause life to work.  It is not wasteful or inneficient.  I absolutely did not believe in junk DNA as was later proved right.  God doesn't make junk and the entire universe is engineered by God to support life.  Understanding this allows you to make discoveries that normal darwinists cannot make as easily in my opinion."
21:09 < klafka_> \LOL
21:09 < klafka_> who is this?
21:09 < kanzure> xp_prg
21:09 < kanzure> perhaps the greatest hplusroadmap troll of all time.
21:09 < archbox_> fenn: amen
21:09 < klafka_> aah
21:10 <@fenn> sometimes i wonder if he's doing it intentionally
21:10 < kanzure> i saw him the other day in another channel (phantomjs)
21:10 < kanzure> he seems to blame all his failure on me :p
21:10 < BioGuy> nmz787: Ya, sorry I don't check my email nearly as often as I would like to, but if your still up for trying to find people into DIYbio in the PDX area I'm definitely up for it
21:10 < BioGuy> Sorry gotta run, lets talk later
21:11 < klafka_> ill be in pdx soonish i think
21:11 < kanzure> klafka_: don't go; if pdx achieves critical mass then there is no way to stop the singularity.
21:11 < klafka_>  haha
21:11 < klafka_> i won't move there
21:11 < klafka_> our company has an office there
21:11 < klafka_> i go every few months
21:15 < nmz787> klafka_: what do you do
21:15 < nmz787> ?
21:18 < nmz787> I wonder if there are poor neighborhoods in PDX that could benefit from mesh networks for wifi internet connectivity
21:18 < kanzure> klafka is a phd student who has chosen the glamorous life of sql monkey
21:19 < kanzure> ryan bethencourt just sent out http://opensourcebiotech.wikia.com/wiki/Main_Page
21:19 < kanzure> wikia :(
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21:20 < nmz787> kanzure: so i guess you don't watch netflix much if you don't know ho you've watched it previously
21:20 < nmz787> kanzure: didn't you mention you were thinking of cancelling it because of ads?
21:20 < kanzure> nmz787: i'd rather not admit to it
21:20 < kanzure> please don't make me admit i watch netflix
21:21 < nmz787> kanzure: !
21:21 < nmz787> kanzure: tell me how you watch netflix
21:21 < kanzure> the things i say in the other channel aren't entirely public statements
21:21 < nmz787> you said it in here
21:22 < kanzure> bryan@gnusha:~/code/paperbot/modules$ grep netflix ~gnusha/public_html/logs/2013* | grep netflix
21:22 < kanzure> nope
21:22 < kanzure> /home/gnusha/public_html/logs/2013-02-08.log:20:35 < nmz787> kanzure: earlier you mentioned netflix i think?
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21:31 < rigel> so anyone here know enough javascript to write a greasemonkey plugin?
21:31 < kanzure> sure, what's up
21:32 < rigel> i was just twittering with carl malamud, who was griping about the us congress's house videos
21:32 < rigel> they're behind a ustream wall, so you cant download them
21:32 < kanzure> there are lots of tools to download crap from ustream
21:32 < rigel> i spent a good bit of time over the summer dicking around trying to pull them down programmatically
21:33 < kanzure> i think cclive supports ustream
21:33 < kanzure> .. maybe.
21:34 < rigel> anyway, it's just this one flash/AMF handshake that needs to be gotten around
21:34 < rigel> and i was thinking maybe a plugin a la archiveteam's JSTOR plugin would be in order
21:35 < rigel> there are a couple of .js AMF packages
21:35 < rigel> all you need to do is get past that handshake and get the direct url
21:35 < kanzure> http://userscripts.org/scripts/show/61384
21:36 < kanzure> by coincidence.. paperbot might be capable of downloading videos from ustream already.
21:36 < rigel> i have already spoken with someone from IA about this, they are perfectly happy to host the videos
21:37 < rigel> they have a whole procedure for bulk uploads
21:37 < kanzure> we have someone from IA in here
21:37 < rigel> it would be great if it could upload it directly
21:38 < kanzure> also #archiveteam on efnet i think
21:38 < rigel> oh, i no longer do efnet
21:38 < klafka_> nmz787: data scientist
21:38 < rigel> i mean its fucking congressional video, it needs to be downloadable, not just streamable
21:41 < rigel> over the summer, i think in part because i was able to tell the guy i was working for how to circumvent the download restrictions on a senate video, he was able to highlight testimony from a particular person, put it on youtube, they got pushback about those statements, a few days later they were retracted
21:42 < rigel> downloading, not just streaming, is fucking KEY
21:42 < rigel> not retracted, but "clarified" i.e. walked back
21:46  * juri_ nods.
21:46 < juri_> that's a worthwhile goal.
21:47 < rigel> so you guys have the brains here
21:47 < rigel> i spent weeks dicking around with the AMF handshake in python
21:47 < rigel> i have some notes i can share but i doubt you'll need them honestly
21:48 < juri_> i'm already way behind, and not making enough money to make ends meet. AND trying to build an aluminium printer.
21:49 < juri_> i are teh smart!
21:49 < rigel> story of my fucking life brah
21:49 < rigel> not the aluminum printer part
21:49 < rigel> i have an exam on monday that i am two weeks behind on studying for, and another on tuesday
21:50  * juri_ nods.
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22:18 < kanzure> nmz787: what seedbox did you get?
22:19 < JayDugger> Good morning, everyohe.
22:19 < JayDugger> everyone.
22:26 < klafka_> lol
22:26 < klafka_> http://madhadron.com/a-farewell-to-bioinformatics
22:27 < klafka_> LOL
22:27 < klafka_> There are only two computationally difficult problems in bioinformatics, sequence alignment and phylogenetic tree construction.
22:27 < klafka_> this guy is hilarious
22:28 < kanzure> klafka_: there were some ok comments about that article here, http://news.ycombinator.com/item?id=5123022
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22:34 < klafka_> interesting
22:38  * klafka_ is he must admit pretty happy to have never gone into bioinformatics fully
22:39 < kanzure> "My friend said: Bioinformatics means that computer scientists – who don't know mathematics and don't know biology – are trying to do mathematical biology."
22:39 < kanzure> that said, there's still a lot of valuable bioinformatics tools i think
22:39 < klafka_> LOL
22:40 < klafka_> to be honest though there is a lot of bullshit here too
22:40 < klafka_> there are fantastic biologists, mathematicians, statisticians, and computer scientists doing good bioinformatics / comp bio / etc...
22:41 < klafka_> i'd point you towards the work that michael jordan has done in proteins and daphne koller in gene network reconstruction
22:41 < klafka_> or ummm basically most of the broad institute is fucking badass
22:41 < kanzure> the michael jordan of proteins, you say?
22:41 < rigel> there was a paper that said bioinformatics was "black magic"
22:41 < klafka_> no he's really the michael jordan of machine learning
22:41 < rigel> which was always my feeling
22:42 < klafka_> i think the most cogent points that rant makes are code reproducibility and experiment reproducibility
22:42 < kanzure> i think the work that open-bio.org does is useful (biopython, bioruby, bioperl, biojava) but a little fragmented
22:42 < klafka_> it is very much the case that microarrays are pieces of shit
22:42 < rigel> if you dont know the algorithms or why youre using them (and 99.9% of working biologists havent the faintest fucking clue what a blast search does other than "find a gene") then you're flying blind. garbage in garbage out
22:42 < kanzure> "If you really want to get a feel for how deluted the Bioinformatics community is, look for a job in the field as an outsider. It's not uncommon to see requirements like: "Must be an expert in 18 technologies" "Must have a PHD in Computer Science or Molecular Biology" "Must have 12 years experience and post doctoral training" "Pay: $30,000""
22:43 < klafka_> rigel: there are a lot of people doing comp bio that know a lot of computer science / math
22:43 < rigel> that's just fine
22:44 < rigel> but when you're a biologist hoping that the computron machine thinger will magically make your results relevant
22:44 < rigel> which is overwhelmingly the case
22:44 < rigel> then it's still shite
22:45 < klafka_> rigel - well first off they are generally not publishing bioinformatics results in those instances - second the problem of experimental design is not a computational problem but really a statistical problem
22:46 < rigel> i would wager that there are no more than 200 working bench lab biologists in the world who have bout 1) used bioinformatics tools in a paper and 2) examined the assumptions underpinning those computational tools to make sure they were appropriate to the work they were doing
22:46 < kanzure> far more than 200 for #1
22:46 < klafka_> yeah so many more
22:46 < rigel> thousands or tens of thousands for just #1, certainly
22:46 < klafka_> also I'm not totally sure #2 is relevant
22:46 < klafka_> wait are you quoting people or making statements ?
22:46 < rigel> making statements
22:47 < klafka_> that you then immediately contradict?
22:47 < rigel> s/bout/both
22:47 < rigel> does that make more sense now?
22:47 < rigel> sorry
22:48 < klafka_> I would make the argument that bench lab biologists don't generally do that anaylsis and directly use those tools
22:48 < kanzure> flikr is really disappointing for queries like "microbes" "protozoa" "microorganism" :( i guess the results for "microscopy" are okay.
22:48 < klafka_> they typically have bioinformatics students / co-authors
22:49 < rigel> you'd be wrong then. maybe better funded labs.
22:49 < klafka_> well I mean prove me wrong
22:49 < rigel> we're both jerking off here then
22:49 < klafka_> anecdotally even in the underfunded bio labs I worked in that was the case
22:49 < klafka_> rigel:  were you involved in biology or bioinformatics from an academic perspective?
22:50 < rigel> the place i worked we had about 30 PIs and maybe 40 assistants of varying levels
22:50 < rigel> not a bioinformaticist in the entire place
22:50 < rigel> all mostly small labs, sometimes just the PI
22:51 < yashgaroth> what academic wetlabs have bioinformatics people just laying around?
22:51 < klafka_> interesting - i've seen that moreso in medical labs
22:52 < klafka_> but anyway I think that a lot of these problems he's describing are really just endemic to academia
22:52 < klafka_> i would lay a lot of the same accusations against computer science as an academic field too
22:53 < klafka_> things like code reproducibility
22:53 < rigel> i think it's just computers, man
22:53 < rigel> they make people stupid
22:53 < rigel> add computers to any endeavor and on some level, it makes people stupider
22:53 < rigel> they think the magic electric box will fix everything
22:54 < rigel> you see it in industry just as much in academia
22:54 < klafka_> yeah kind of - though i feel people are much more constrained by costs in the real world
22:54 < klafka_> or industry
22:55 < rigel> well, shitting the bed has much more palpable effects because it's not part of, you know a societal grand bargain to have centers of industry or anything
22:55 < rigel> even though it is, really, that protection is only afforded the Big Guys
22:55 < rigel> Too Big To Fail
22:58 < nmz787> heh, michael jordan of proteins
22:59 < nmz787> space jamz is about molecular crowding and binding pockets
22:59 < nmz787> 'the incoming nucleotide dunks into the polymerase!'
23:00 < klafka_> no michael jordan did great work on proteins
23:00 < klafka_> http://videolectures.net/nips2010_jordan_sip/
23:06 < kanzure> http://videolectures.net/Top/Biology/Neuroscience/
23:06 < kanzure> that site makes no sense
23:06 < kanzure> these thumbnails of videos are awful
23:06 < kanzure> the title is more important
23:15 < nmz787> klafka_: i'm laughing at a mental molbio mashup of this http://en.wikipedia.org/wiki/Space_Jam
23:15 < klafka_> haha
23:16 < nmz787> in the multiple world interpretation...
23:17 < klafka_> INFO:s3-mp-upload:Finished uploading 1546.04M in 7.84s (197.24Mbps)
23:17 < nmz787> i think that's exceeding the legal speed limit
23:17 < nmz787> :p
23:37 < klafka_> http://www.wired.com/opinion/2013/02/big-data-means-big-errors-people/
23:37 < klafka_> LOL
23:38 < klafka_> this article i think is even worse
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--- Log closed Sat Feb 09 00:00:55 2013